In michbur/tidysq: Tidy Processing and Analysis of Biological Sequences

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tidysq

Overview

tidysq contains tools for analysis and manipulation of biological sequences (including amino acid and nucleic acid -- e.g. RNA, DNA -- sequences). Two major features of this package are:

• effective compression of sequence data, allowing to fit larger datasets in R,

• compatibility with most of tidyverse universe, especially dplyr and vctrs packages, making analyses tidier.

Getting started

Try our quick start vignette or our exhaustive documentation.

Installation

The easiest way to install tidysq package is to download its latest version from CRAN repository:

install.packages("tidysq")

Alternatively, it is possible to download the development version directly from GitHub repository:

# install.packages("devtools")
devtools::install_github("BioGenies/tidysq")

Example usage

library(tidysq)

file <- system.file("examples", "example_aa.fasta", package = "tidysq")
sqibble <- read_fasta(file)
sqibble

sq_ami <- sqibble$sq
sq_ami

# Subsequences can be extracted with bite()
bite(sq_ami, 5:10)

# There are also more traditional functions
reverse(sq_ami)

# find_motifs() returns a whole tibble of useful informations
find_motifs(sqibble, "^VHX")

An example of dplyr integration:

library(dplyr)
# tidysq integrates well with dplyr verbs
sqibble %>%
  filter(sq %has% "VFF") %>%
  mutate(length = get_sq_lengths(sq))

Citation

For citation type:

citation("tidysq")

or use:

Michal Burdukiewicz, Dominik Rafacz, Laura Bakala, Jadwiga Slowik, Weronika Puchala, Filip Pietluch, Katarzyna Sidorczuk, Stefan Roediger and Leon Eyrich Jessen (2021). tidysq: Tidy Processing and Analysis of Biological Sequences. R package version 1.1.3.

michbur/tidysq documentation built on Jan. 2, 2025, 10:41 p.m.